Minian, an open-source miniscope analysis pipeline

Dong, Zhe; Mau, William; Feng, Yu; Pennington, Zachary T.; Chen, Lingxuan; Zaki, Yosif; Rajan, Kanaka; Shuman, Tristan; Aharoni, Daniel; Cai, Denise J.

doi:10.7554/elife.70661

Cited by 40 publications

(18 citation statements)

References 49 publications

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“…To extract calcium transients from the calcium imaging data, we employed our previously published open-source calcium imaging data processing pipeline, Minian 70 . Briefly, videos were pre-processed for background fluorescence and sensor noise, and motion corrected.…”

Section: Methodsmentioning

confidence: 99%

Aversive experience drives offline ensemble reactivation to link memories across days

Zaki

Pennington

Morales-Rodriguez

et al. 2023

Preprint

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Memories are encoded in neural ensembles during learning and stabilized by post-learning reactivation. Integrating recent experiences into existing memories ensures that memories contain the most recently available information, but how neural ensembles accomplish this critical process remains unknown. Here we show that in mice, a strong aversive experience drives the offline ensemble reactivation of not only the recent aversive memory but also a neutral memory formed two days prior, spreading the fear from the recent aversive memory to the previous neutral memory. We find that fear specifically spreads retrospectively, but not prospectively, to neutral memories across days. Consistent with prior studies, we find reactivation of the recent aversive memory ensemble during the offline period following learning. However, a strong aversive experience also increases co-reactivation of the aversive and neutral memory ensembles during the offline period. Finally, inhibiting hippocampal reactivation during this offline period abolishes the spread of fear from the aversive experience to the neutral memory. Taken together, these results demonstrate that strong aversive experience can drive retrospective memory integration through the offline co-reactivation of recent memory ensembles with memory ensembles formed days prior, providing a neural mechanism by which memories can be integrated across days.

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Section: Methodsmentioning

confidence: 99%

Aversive experience drives offline ensemble reactivation to link memories across days

Zaki

Pennington

Morales-Rodriguez

et al. 2023

Preprint

Self Cite

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“…We suppressed these artefacts by sequentially applying a high-pass (with a cut-off of 0.5-Hz) and smoothing with a moving average filter of 10 samples (cut-off of 2-Hz). Motion artefacts present in miniscope configurations associated with relative movement of the sensor and the brain( 60 ) do not occur with the SCOPe device because it is in direct contact with the cortical surface.…”

Section: Resultsmentioning

confidence: 99%

Subdural CMOS optical probe (SCOPe) for bidirectional neural interfacing

Pollmann

Yin

Uguz

et al. 2023

Preprint

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Optical neurotechnologies use light to interface with neurons and can monitor and manipulate neural activity with high spatial-temporal precision over large cortical extents. While there has been significant progress in miniaturizing microscope for head-mounted configurations, these existing devices are still very bulky and could never be fully implanted. Any viable translation of these technologies to human use will require a much more noninvasive, fully implantable form factor. Here, we leverage advances in microelectronics and heterogeneous optoelectronic packaging to develop a transformative, ultrathin, miniaturized device for bidirectional optical stimulation and recording: the subdural CMOS Optical Probe (SCOPe). By being thin enough to lie entirely within the subdural space of the primate brain, SCOPe defines a path for the eventual human translation of a new generation of brain-machine interfaces based on light.

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“…Analysis of imaging data: Imaging data were analyzed using custom Python scripts based on the Minian pipeline. 98 Imaging data was registered to collect for motion artifacts and denoised using a median filter. A constrained non-negative matrix factorization (CNMF) algorithm was used to identify single cells and extract calcium activity.…”

Section: Methods Detailsmentioning

confidence: 99%

Vagal interoception of microbial metabolites from the small intestinal lumen

Jameson,

Kazmi,

Son

et al. 2023

Preprint

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SUMMARYThe vagus nerve is proposed to enable communication between the gut microbiome and brain, but activity-based evidence is lacking. Herein, we assess the extent of gut microbial influences on afferent vagal activity and metabolite signaling mechanisms involved. We find that mice reared without microbiota (germ-free, GF) exhibit decreased vagal afferent tone relative to conventionally colonized mice (specific pathogen-free, SPF), which is reversed by colonization with SPF microbiota. Perfusing non-absorbable antibiotics (ABX) into the small intestine of SPF mice, but not GF mice, acutely decreases vagal activity, which is restored upon re-perfusion with bulk lumenal contents or sterile filtrates from the small intestine and cecum of SPF, but not GF, mice. Of several candidates identified by metabolomic profiling, microbiome-dependent short-chain fatty acids, bile acids, and 3-indoxyl sulfate stimulate vagal activity with varied response kinetics, which is blocked by co-perfusion of pharmacological antagonists of FFAR2, TGR5, and TRPA1, respectively, into the small intestine. At the single-unit level, serial perfusion of each metabolite class elicits more singly responsive neurons than dually responsive neurons, suggesting distinct neuronal detection of different microbiome- and macronutrient-dependent metabolites. Finally, microbial metabolite-induced increases in vagal activity correspond with activation of neurons in the nucleus of the solitary tract, which is also blocked by co-administration of their respective receptor antagonists. Results from this study reveal that the gut microbiome regulates select metabolites in the intestinal lumen that differentially activate chemosensory vagal afferent neurons, thereby enabling microbial modulation of interoceptive signals for gut-brain communication.HIGHLIGHTSMicrobiota colonization status modulates afferent vagal nerve activityGut microbes differentially regulate metabolites in the small intestine and cecumSelect microbial metabolites stimulate vagal afferents with varied response kineticsSelect microbial metabolites activate vagal afferent neurons and brainstem neurons via receptor-dependent signaling

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Minian, an open-source miniscope analysis pipeline

Cited by 40 publications

References 49 publications

Aversive experience drives offline ensemble reactivation to link memories across days

Aversive experience drives offline ensemble reactivation to link memories across days

Subdural CMOS optical probe (SCOPe) for bidirectional neural interfacing

Vagal interoception of microbial metabolites from the small intestinal lumen

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